Human-specific tandem repeat expansion and differential gene expression during primate evolution

THIS DATASET IS PART OF THE FOLLOWING STUDY:
https://www.pnas.org/content/early/2019/10/22/1912175116

THE RAW SEQUENCING 10x GENOMICS READS CAN BE DOWNLOADED FROM SRA:
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056

ORIGINAL UPLOAD: 09/06/2019

UPDATES: 10/28/2019; 01/27/2020

DESCRIPTION: Contigs were assembled using Phased-SV (Chaisson et al, Nature Communications 2019) on six human haplotypes (i.e., H0 and H1 in NA19240, HG00514, and HG00733), and six nonhuman haplotypes (this study, H0 and H1 in Clint the chimpanzee, Kamilah the gorilla, and Susie the orangutan). The long read data (PacBio CLR) from NHPs were phased into haplotypes H0 and H1 using linked reads from 10X Genomics prior to assembly, whenever possible. If not possible (e.g., in the case of long runs of homozygosity regions), long reads from both haplotypes were used to generate a "squished assembly". Using human haplotype data, we identified  21,442 polymorphic STRs/VNTRs, followed by a targetted phasing of these regions in the three NHPs. All of the human and nonhuman primate contigs were padded by 2 kbp both upstream and downstream, followed by mapping against the human reference (GRCh38). We did the same for "squished assemblies" from a Yoruban individual, CHM13, and three NHPs as described in Kronenberg et al, Science 2018. The BAM and BAI files in this dataset contain the alignment of all these contigs against GRCh38.